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Castro was signed by scout Jose Serra for the Chicago Cubs in October 2006. In 2007, he hit .299/.371/.371 for the DSL Cubs with 13 steals in 15 tries and 47 runs in 60 games. The next year, Castro batted .311/.364/.464 for the AZL Cubs while splitting time between second base and shortstop; Baseball America rated him the #14 prospect in the Arizona League and #7 Cubs prospect.

In 2010, he started the year with the AA Tennessee Smokies and tore up the Southern League (.376/.421/.569, 20 R, 20 RBI in 26 games) before being called up to Chicago on May 7. His major league debut that day was a memorable one. Playing the Cincinnati Reds, he hit a three-run homer off Homer Bailey in his first major league at-bat, then added a bases-loaded triple as the Cubs defeated the Reds, 14-7. At age 20, he was the youngest shortstop in Cubs history, the first player born in the 1990s to play in the major leagues, and only the 6th player to homer in his first major league at-bat for the team; the last had been pitcher Jim Bullinger in 1992. Even more remarkably, his 6 RBI were an all-time record; a number of players had driven in five runs in their major league debut, most recently Ben Grieve in 1997, but none had ever had 6. While he had been considered Chicago's top prospect, the power display was a surprise as he had homered 9 times in 995 minor league at-bats. However, his Wrigley Field debut on May 10 was less of a fairy tale: he committed three errors in a 4 - 2 loss to the Florida Marlins and was booed by his hometown fans. He settled nicely into the Cubs' regular shortstop job after that, and was still hitting over .300 in mid-August. He finished the season hitting an even .300 in 125 games, with a .345 OBP and a slugging percentage of .408. His ability to hold his own in the major leagues at such a young age made him one of the most promising rookies of the year, and earned him a spot on the 2010 Topps All-Star Rookie Team.

Castro was back as the Cubs' starting shortstop in 2011 and was one of the few bright spots on a team that under-performed significantly in spite of a large payroll. He was named to the 2011 All-Star Game as the Cubs' sole representative. However, he also got in trouble with manager Mike Quade for his sometimes lackadaisical play. The last straw came on August 21st, when he was goofing around and had his back to the plate when James Russell delivered a 6th-inning pitch against the St. Louis Cardinals. Quade benched his young star the next day and had him apologize to his teammates. Castro vowed "it would never happen again". He finished the season with 207 hits, the most in the National League and also led the circuit in at-bats and singles while posting a .307 batting average. Following the season, Chicago police announced that they were investigating charges of sexual assault filed against Castro, but dropped the case in April after finding insufficient evidence to move forward with a prosecution. He got into more trouble with a manager in 2012, this time rubbing new skipper Dale Sveum the wrong way. A key incident occurred on June 4th, when he forgot how many outs there were in the 5th inning and started to jog off the field after receiving a toss from 2B Darwin Barney, never attempting to complete the double play that would have gotten the Cubs out of the inning. The San Francisco Giants took advantage of the blunder to tie the game, which they eventually won, 3-2. Sveum was furious after the game calling the play "the last straw". "These things have got to stop happening," he added, "or we're just going to stop playing him. It's something obviously that's unacceptable at any time." All of that frustration seemed to be forgotten by the end of August, though, when the Cubs announced that they had signed their young star to a seven-year extension worth $60 million; the deal also included an option for 2020, making Castro a cornerstone of future Cubs teams. General Manager Jed Hoyer explained that Starlin was a special talent, having established himself as a major leaguer at 20, and as a reliable veteran at the tender age of 22, adding "He's one of the players we're building around." On September 7th, he collected the 500th hit of his career, becoming only the 28th player in major league history to do so before the age of 23, and the first since Alex Rodriguez. he played all 162 of the Cubs' games that season, leading the NL with 646 at bats. He collected 183 hits, scored 78 runs and drove in as many, while amassing 29 doubles, 12 homers and 14 triples. His batting average fell to .283 and while he stole 25 bases, he was caught a league-leading 13 times.

In 2013, he had his first poor season as the Cubs continued to struggle on the field, falling to last place following the departure of the Houston Astros from the NL Central. While Castro continued to play everyday (161 games) and again led the NL in at-bats, he hit only .245, but with an OBP of .284 only. He continued to hit doubles (34), but only had 2 triples and 10 homers. As a result, he scored only 59 runs and drove in 44, while his OPS+ was a poor 72, his first season below 100. Following the season, he became locked in a legal dispute with the baseball academy which had nurtured him in the Dominican Republic. The "Mi Futuro Biliguer" Academy had $3.7 million seized from Castro's bank account, claiming that when he was 15 years old, his father had enrolled him with the promise that he would return 3% of his son's future major league earnings to the school. Castro had made payments to the school in the past, but stated that he did not consider himself bound in perpetuity.

He had a nice bounce-back season in 2014, returning to the All-Star Game after missing out the previous season. The Cubs started out the season struggling, but the excitement returned as they started promoting some of their top minor league prospects to the majors, creating excitement among the public at Wrigley Field. Castro was one of the few veterans around which the Cubs wanted to build, although he was also feeling the pressure of the coming wave, as two of the young prospects ready to help the big league club were natural shortstops: Javier Baez and Addison Russell. At first, Baez played second base after being called up, with Castro keeping his shortstop job, but on September 2nd, he sprained his ankle sliding into home plate, likely ending his season, He was hitting .292/.339/.438 in 134 games, with 33 doubles and 14 home runs. He had been moved from the lead-off spot to a slot in the middle of the line-up, and as a result had seen his runs scored go down to 58 but his RBI increase to 65, while his OPS+ was his highest yet at 113.

On December 27, 2014, Castro was questioned by police following a shooting at a nightclub in his hometown of Monte Cristi. Castro explained through his agent that he was present during the incident but was not involved in any way. He played 151 games for the suddenly competitive Cubs in 2015, starting the season at shortstop and eventually moving over to second base as rookie Addison Russell took over shortstop. Starlin hit .265 with 23 doubles and 11 homers, scored 52 runs and drove in 59 as his OPS+ fell to 83. At 25, he was one of the most experienced position players on a very young Cubs team. In the first taste of postseason of his career, he went 0 for 4 against the Pittsburgh Pirates in the Wild Card Game, then hit .286 (4 for 14) as the Cubs surprised the St. Louis Cardinals in the Division Series. However, he was only 2 for 16 when they were eliminated by the New York Mets in the NLCS. On December 8th, the Cubs signed free agent Ben Zobrist to a large contract, and to open up the starting second base job for him, traded Castro to the New York Yankees in return for P Adam Warren and a player to be named (Brendan Ryan).

On May 29, 2016, he got the Yankees' only hit of the game as they faced the Tampa Bay Rays and Jake Odorizzi. Castro's safety was a two-run homer in the 7th inning, and it was enough to give New York a 2-1 victory, the first time the Yankees had won a game with only one hit since 1914, and in that case it had been in a game cut short to six innings by darkness.